Welcome to the Necro Files, just off Highway 666. Follow the trail of general debauchery and complete and utter murder and mayhem. Reviews of top horror movies. Reviews of albums by top heavy metal bands. Do not feed the Garg!

06 December 2008

How Random is Random Mutation on DNA?

"If we want to postulate a deity capable of engineering all the organized complexity in the world, either instantaneously or by guiding evolution, that deity must have been vastly complex in the first place.

The creationist, whether a naive Bible-thumper or an educated bishop, simply postulates an already existing being of prodigious intelligence and complexity."Richard Dawkins

This post forms part of a series on Mr Marshall's Random Mutator. You can find all the posts here:

What is mutation?

Simply put, a mutation is a change in the nucleotide sequence of the genetic material of an organism. This genetic mutation could cause changes in the phenotype of your species. For example, you could have a mommy and a daddy with blue eyes who give birth to a child with brown eyes.

What causes mutation?

"Mutations can be caused by copying errors in the genetic material during cell division, by exposure to ultraviolet or ionizing radiation, chemical mutagens, or viruses, or can be induced by the organism, itself, by cellular processes such as hypermutation."[Mutation, Wikipedia]

Copying errors, you say? One would think that a system intelligently designed by an omniscient, omnipotent deity would not be prone to copying errors. It surely wouldn't be sensitive to ultraviolet radiation either, given that an omniscient deity would've seen that one coming.

Similarly, if mutations were not random, but predicted and designed by a perfect designer, one would expect that these errors would not be copied over to the next generations, but that some error-correcting mechanism would be in place. This would ensure that if you exercised your free will too leniently and you ended up next to a UV light for too long that your children and your children's children are at least protected from your inability to practice sound discrimination towards malignant types of light sources.

Do mutations in DNA occur randomly and indiscriminately?

This is exactly what Mr Marshall's random mutator suggests. However, in DNA, you don't have one string, like you do in Mr Marshall's random mutator. You have two strands. Both strands consist entirely of the letters A, C, G and T. An A on the one string mostly (but not necessarily) corresponds to a T on the other strand, and vice versa. A C on one strand mostly (but not necessarily) corresponds to a G on the other strand, and vice versa. More significantly, any possible combination of A, C, G and T is a proverbial word in the language of DNA.

This is important, because not all combinations of letters in Plain English are words. Mr Marshall would do well to model his random mutator so that it bewares of the Jabberwocky. At least this would resemble the working of one strand of DNA somewhat. Since any combination of letters in the DNA alphabet form meaningful words in the genetic code, there is no possibility that a random mutation would prevent your genetic information from being transferred. It follows that the randomness of mutation in DNA is immaterial, because no mutation would cause your organism to necessarily become extinct.

A Cro-magnon skull. Mr Marshall's random mutator reasons that natural selection implies that we can revert our current human population back to Cro-magnons, and if we can't evolve to our current level of humanity, humanity would necessarily become extinct.

Mutation does occur randomly, but not indiscriminately thanks to natural selection. A mutation in some of your DNA is not necessarily a mutation in all of your DNA, or in all of the DNA of a particular species, as only the mutations which get passed on to your offspring are relevant. Mr Marshall's mutator does not model this scenario at all, but his model implies that any random mutation in the DNA of a particular organism automatically occurs species wide.

Mr Marshall's random mutator does not model natural selection

Mr Marshall reasons that since you can mutate randomly and then revert back to your selected text, his mutator does model natural selection. I fail to see how taking modern day humans and reverting us back to archaic homo sapiens has anything to do with natural selection. Besides, his 'Revert To Selected Text' button does not in fact revert back to selected text. It entirely clears the text. As an information scientist, Mr Marshall should surely be aware of Nielsen's heuristics. Poor user interface design does nothing to bring your point across more clearly.

Natural selection is not a carefully designed, directed process. Nor is it capable of being completely ignored in a model of mutation. Sticking with Darwin's definition:

"One general law, leading to the advancement of all organic beings, namely, multiply, vary, let the strongest live and the weakest die".[Wikiquote, Charles Darwin]

There is nothing in this mutator that models selecting the strongest letters, words or sentences, and letting the weakest letters, words or sentences die. Note that this mechanism does not imply a designer. This mechanism could be brought about by an outbreak of Aids in your population.

Surely, if your DNA were designed by a perfect, omniscient deity, she would've seen that one coming too? Why then are some people immune to Aids while others are not? Why then are some more immune to malaria, while others are not? Natural selection seems to explain that, without the need for a designer. Mr Marshall's random mutator does not.

By the way, I haven't mentioned Cthulhu in this post. I just thought I'd randomly mention that.

This is the first time i came to your blog and i must say i like it alot! Specially the articles. I would like to suggest you to add your articles to www.add-article.info. It's a site where people go to find articles. So i suggest you go there and register. Once you register, you can add descriptions of your articles in less than 30 seconds. By doing that, you will recieve two links to your blog and a picture of your blog next to the description. That way people will find your blog and you will get many new visitors. Do not forget to vote for your articles after you add them to that site, that way you will be on the first site for a long time (tell others to vote too).

Well anyhow, hope to see you there soon :-) , if not, good luck with your articles and keep up with good work.Cheers,Matt

You try your best, but as usual, that people are on one or the other camp, they use mathematical arguments (here randomness) not in scientific way but in social way, that is trying to prove what you are already convinced to prove. As I put it on Blogcatalog, one can go around this a long time because we do not take into account this: the singularity of the event of life's apparition. All the arguments we use are for after life apparition ( same for the Universe) that is it's fundamentally flawed.

As to come back to statistics, I put it again from what I posted on Blogcatalog:

As I've been a scientist in Statistic and Biology I would say that asking and answering the question the simplistic way are the primary reason people keep biaised on both sides.

Is DNA random is like asking is Stock Market Random ? According to so called Efficiency Market Theory, stock market is Random but this is an orthodoxy point of view to justify the so-called "FREE" market theory whereas any real world stock market professionals know the stock market is from time to time hit by an event which on paper would not occur with a probability higher than 1 over dozens of thousand years whereas it occurs almost every 3-4 years.

Why, because people use theory without rigor, randomness refers to Normal Law which comes itself from Central Limit Theorem which states that it is true only if factors are small and independant. In the stock market this cannot be true as there are huge players that weight on the market, in the case of DNA this can surely be not true either because of the environment conditions.

That is at this level of debate, one or the either camp cannot prove much.

Ryan Whittal here. A small theological matter. I like your knowledge of science thus far...

You said...

Copying errors, you say? One would think that a system intelligently designed by an omniscient, omnipotent deity would not be prone to copying errors. It surely wouldn't be sensitive to ultraviolet radiation either, given that an omniscient deity would've seen that one coming.

The Fall, Garg, The Fall. Perfect Creation and then death and decay post Fall. It shows your anti-Creation agenda (and Biblical ignorance). Please read the fist 10 chapters of Genesis for clarity.

Surely, if your DNA were designed by a perfect, omniscient deity, she would've seen that one coming too? Why then are some people immune to Aids while others are not? Why then are some more immune to malaria, while others are not? Natural selection seems to explain that, without the need for a designer. Mr Marshall's random mutator does not.

An answer to your theological problem: Perfect creation followed by the Fall...(YAWN)

Hi RyanSo you have a perfect, flawless creation. That makes a huge mistake called The Fall. That is called a paradox. It means either the creation was not flawless.

I've read the entire Bible, quite a few times. The Bible is a religious work and does not tell us anything about microwaves or silicon chips. Neither does it give us a creation account that agrees with the available evidence.

The fall does not explain why DNA makes copying errors. However, if you consider the weak bonds between DNA chains, and that they sometimes get a bit of push and pull that doesn't always give you a deterministic outcome, it's a plausible explanation for copying errors. Especially when one considers the immense size of a DNA strand (relative) and the immense amount of information that is contained in it.

It is the sheer size of it that ensures copying errors are of no consequence most of the time. It is also partially the copying errors that ensure mutation.

Hi RyanYou can subscribe to comments, in which case you'd get a notification when new comments are made.

If you read the entire link that I posted, you'd find an explanation for the concept of speciation. Speciation is the process whereby new species arise. New species here depends on your criteria for species, but however Creationists or IDiots define it, the evidence is there.

The Talk Origins website also explains evolution.

And you just tacitly admitted evolution.

You must excuse me, from your evident ignorance of biology I was under the impression that you are keen to learn more about the subject. I was catechised, with the main purpose of making an informed decision regarding religion. This greatly contributed to my atheism. Like they say, if more people read the Bible, there would be more atheists.